System level diagnosis is an abstraction of high level and, thus, its practical implementation to particular cases of complex systems is the task which requires additional investigations, both theoretical and modeling. Mostly, diagnosis at system level intends to identify only permanently faulty units. In the paper, we consider the case when both permanently and intermittently faulty units can occur in the system. Identification of intermittently faulty units has some specifics which we have considered in this paper. We also suggest the method which allows distinguishing among different types of intermittent faults. Diagnosis procedure was suggested for each type of intermittent faults.